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On global sequence alignment
Abstract
We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.
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Citations
Cited by
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
Self-citationThe genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139
Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A. J., Müller, W. E. G., Wetter, T., & Suhai, S. (2004) · Genome Research · doi:10.1101/gr.1917404 · Cited by 1,050
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
SPARC, a matricellular protein: at the crossroads of cell–matrix communication
Brekken, R. A., & Sage, E. H. (2001) · Matrix Biology · doi:10.1016/s0945-053x(00)00133-5 · Cited by 585
Metadata
- Authors
- Huang, X.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 1994
- Volume
- 10
- Issue
- 3
- Pages
- 227-235
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2143464518
- Cited by
- 224
- References
- 0
- FWCI
- 3.19
- Type
- journal article
- Language
- en
- Open access
- closed
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